mmhhh...
1) Useless NPC. Well, someone that says: I'm an Error could be cute, but I don't need in every damn village someone that says: We are in XYZ! Yeah... Great. So what? Want a cookie now you said that? And there are games where almost all npc are useless. They don't give you quests, they don't give you items for free or they don't sell you something. And they don't give you any clues on your quest or subquest, like: I heard that there's an island in the middle of the world were you may find nothing but a key in the sand which open things in the world.
For me, characters should do things. Yes they may "Hi!" you too, but when the story goes on they could change the script.
2) Have to level up like a bodybuilder filled with steroids because "that" particular pink slime kicks you everytime and you can't go on because it even blocks your way. Just why?
3) Useless tech. Like the power pumping up of the mightyness that rise your stats by the incredible value of 2 points. I like more skills that improve and don't waste space in the menu. I won't use Fire for the rest of my life, I'd like to do more damage, so, if I have Fire level Burning Hell, why I have to keep Fire level campfire?
4) Useless classes. In FFV there were classes that were like useless. Like berserker. Or beastmaster. You had to master them for completition, but, seriously, who ever used them then?
5) Awful maps. I hate starting a game with a good story to find maps 50x50 or 100x100 full of nothing. And I found them. I just stop to play. I can't just walk for hours to get somewhere. Or interior with 4-walls and things scattered on the floor randomly. In every room. Worst if you have to explore and "click" on things to gather items. How can I know what I have to "click" to find things if on the floor there are 24835928 objects? Not counting the 3247 windows and wall things.
6) Useless quests. Some dumb quest like: get me 5 bouquets are ok and I'll give you 1 potion are ok, to get confidence with quest system, but when you have to slay the overlord you can stop to do quest for 100 gold, a potion or a wooden sword. More if you have to go up and down everywhere and in places where you couldn't survive 'till a certain level. Like: yeah destroy a thousand dragons of doom. They are scattered in as many towers. The reward is a piece of cloth you can use to... do nothing. Yeah... Someone are fun, someone not.
7) Boring items. Like phoenix down to revive people or echo herb. In non FF games or non commercial games like rpg maker ones. In FF I expect them, but in amatorial games or games made by others I expect some originality.
Well actually a lot of things. There are surely others, but those are the first ones I can think of.